"Let me explain something. Deep-dish pizza is not only not better than New York pizza — it's not pizza," said Stewart, calling it "tomato soup in a bread bowl. ... I don't know whether to eat it, or throw a coin in it and make a wish."

Some upset Chicagoans made their own wishes — which can't be repeated here.

"Nearly 9 percent of orders are deep-dish or stuffed pizza. So anything that's not a deep-dish pizza is 10 times more popular in the city of Chicago," says Mack. "Think about it: If you were to order pizza every day for 10 days, how could you possibly eat deep-dish pizza more than once? Good luck."

But Darren Tristano, a food industry researcher at Chicago-based Technomics, questions the data, noting that GrubHub's users tend to be younger with less money to spend. And yes, deep dish is more expensive.

And there's this: Not even half of the pizzerias for which GrubHub has data in Chicago offer deep dish on the menu.

GrubHub also doesn't include local deep-dish chains like Giordano's and Lou Malnati's. Those two chains have a combined 20 restaurants in Chicago — and sell three times as much deep dish as thin crust.

But a look at the city's history raises some questions about Chicago's true pizza legacy.

Porter says tavern-style pizza, the type cut into squares, was developed on the South Side of Chicago to keep working men in taverns. Free pizzas would go out on the bar, and the workmen would snack on it and stay there for an extra hour or two. It made all the difference in how much beer they drank.

"And that's one of the styles that we grew up with. I didn't even really have deep dish until I was almost in high school," Porter says. "So I truly do feel that the thin-crust tavern-style is the true Chicago style."

Marc Malnati, the fourth-generation owner of deep-dish chain Lou Malnati's, doesn't agree. He brokered an on-air truce with Stewart over one of his deep-dish pizzas.

"I think that the deep-dish pizza has been and always will be Chicago's pizza," Malnati says.

JOHN: So GrubHub's users tend to be younger, with less money to spend. But other food industry researchers know that of the roughly 600 pizzerias in town, fewer than half even offer deep dish on the menu.

Then again, local pizza chains like Giordano's and Lou Malnati's do. GrubHub doesn't include them in its data. But they sell three times more deep dish than thin crust.

So this pizza puzzle is far from solved. There might be a clue at Pizano's Pizza and Pasta in the Loop, one of the pizzerias in GrubHub's data set. It sells both deep dish and thin crust.

Waiter Terry Morrison has a clear favorite.

TERRY MORRISON: I grew up in Chicago, so I don't ever really jones for, like, deep dish pizza, I'd rather just have a thin crust.

JOHN: Maybe thin crust is more popular for the people who actually live here.

JON PORTER: I mean, I truly do feel that the thin crust tavern style is the true Chicago style.

JOHN: Jon Porter runs Chicago Pizza Tours, and Pizano's is one of his regular stops. Porter says long before deep dish, Chicago invented the tavern-style thin crust pizza, the one cut into squares.

PORTER: It was developed on the South Side of Chicago to keep the working man at the taverns. And just, you know, free pizzas would go out on the bar, and they'd just snack on them and they'd stay there an extra hour or two. It made all the difference in how much beer they drank.

JOHN: So, maybe we're just witnessing a Chicago thin crust comeback?

Not so fast, says Marc Malnati.

MARC MALNATI: I think that the deep dish pizza has been and always will be Chicago's pizza.

JOHN: Malnati is the 4th generation owner of Lou Malnati's, and the guy who delivered a deep dish pizza to Jon Stewart a few days after the infamous rant.

(SOUNDBITE OF TV SHOW, "THE DAILY SHOW")

STEWART: It's very, very tasty, and I apologize, you know? Truce.

MALNATI: All right.

STEWART: A truce: Chicago and New York.

JOHN: At his suburban headquarters this week, Malnati joined workers in packing up boxes and boxes of frozen pizzas.

That is a lot of pizza, sir.

MALNATI: It's a lot of pizzas, probably about 1,700 per truckload.

JOHN: More than 10,000 pizzas that day alone, arriving just before Christmas.

MALNATI: This will be our biggest shipping day of all time.

JOHN: But guess what? All those deep-dish pizzas are headed out of town.